New Technology Reveals Secrets of Evolving 30-Year-Old Bacteria

In a paper published in the current issue of Nature, the Michigan State University John Hannah Distinguished Professor of Microbiology and Molecular Genetics and an international team of researchers used cutting-edge technology to study tens of thousands of generations of E. coli bacteria. They sequenced the entire genomes, or genetic code, of the bacteria to pinpoint the genes with beneficial mutations that gave the bacteria a competitive edge over their ancestors.

The bacteria from different generations of the LTEE have been stored in freezers for nearly 30 years, but they were brought back to life to look for the changes in their DNA. Being able to go back into the freezer to study samples from years ago is one of the reasons Lenski calls the LTEE “the experiment that keeps on giving.”

“One of the nice things about such a long-term experiment is that new technologies come along that didn’t exist when I started the LTEE in 1988,” said Lenski, who’s part of MSU’s BEACON Center for the Study of Evolution in Action. “The first bacterial genome was not sequenced until 1995, and now, in this single paper, we’ve sequenced 264 complete genomes from this one experiment.”

The team sequenced hundreds of E. coli genomes to examine how the bacteria had changed in their DNA over 50,000 generations. The researchers found more than 14,000 changes across the LTEE’s 12 populations. Each population changed in different ways, but there were some important commonalities as well.

Most significant, and most simply, the mutations were concentrated in a subset of the genes – those where mutations gave the bacteria a competitive edge. One of the striking differences that arose between populations is that half of them evolved to mutate at much higher rates than the other populations, even though they all started from the same ancestral strain that had a low mutation rate.

“Even in the simplest microcosm we can imagine to study evolution – a single bacterium kept in the laboratory under monotonous conditions for years – we are learning new things about the rates and processes of evolution,” said Jeffrey Barrick, an assistant professor of molecular biosciences at the University of Texas at Austin. “This quantitative information is important for human health, as it improves our ability to predict how bacteria evolve, particularly in chronic infections and in our microbiome.”

This paper is the product of several wonderful collaborations, Lenski said. Noah Ribeck, MSU postdoctoral researcher, developed some of the mathematical theory used to interpret the data. Barrick, a former MSU postdoc in Lenski’s lab, created software for analyzing the genomes. Olivier Tenaillon, with Universite Paris Diderot (France), helped lead the study. Researchers from University of Massachusetts, ETH Zurich (Switzerland), Universite Grenoble Alpes (France), Institut de Genomique (France), and Centre National de la Recherche Scientifique (France) also contributed to this research.

Lenski’s long-term evolution experiment has now surpassed 65,000 generations. His research is funded in part by the National Science Foundation.